+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8hf0 | ||||||
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タイトル | DmDcr-2/R2D2/LoqsPD with 50bp-dsRNA in Dimer state | ||||||
要素 |
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キーワード | RNA BINDING PROTEIN/RNA / Ribonuclease / DOUBLE STRANDED RNA / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 follicle cell of egg chamber stalk formation / lncRNA catabolic process / : / positive regulation of Toll signaling pathway / regulatory ncRNA processing / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / female germ-line stem cell asymmetric division / PKR-mediated signaling / regulation of regulatory ncRNA processing ...follicle cell of egg chamber stalk formation / lncRNA catabolic process / : / positive regulation of Toll signaling pathway / regulatory ncRNA processing / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / female germ-line stem cell asymmetric division / PKR-mediated signaling / regulation of regulatory ncRNA processing / dsRNA transport / dosage compensation by hyperactivation of X chromosome / RISC complex binding / global gene silencing by mRNA cleavage / germ-line stem cell population maintenance / ribonuclease III / apoptotic DNA fragmentation / RISC-loading complex / miRNA metabolic process / deoxyribonuclease I activity / detection of virus / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / ribonuclease III activity / siRNA binding / pre-miRNA processing / siRNA processing / ATP-dependent activity, acting on RNA / positive regulation of innate immune response / RISC complex / positive regulation of defense response to virus by host / heterochromatin formation / helicase activity / central nervous system development / locomotory behavior / mRNA 3'-UTR binding / cellular response to virus / cytoplasmic ribonucleoprotein granule / double-stranded RNA binding / defense response to virus / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Drosophila melanogaster (キイロショウジョウバエ) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.72 Å | ||||||
データ登録者 | Su, S. / Wang, J. / Wang, H.W. / Ma, J. | ||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Structural mechanism of R2D2 and Loqs-PD synergistic modulation on DmDcr-2 oligomers. 著者: Ting Deng / Shichen Su / Xun Yuan / Jinqiu He / Ying Huang / Jinbiao Ma / Jia Wang / 要旨: Small interference RNAs are the key components of RNA interference, a conserved RNA silencing or viral defense mechanism in many eukaryotes. In Drosophila melanogaster, Dicer-2 (DmDcr-2)-mediated ...Small interference RNAs are the key components of RNA interference, a conserved RNA silencing or viral defense mechanism in many eukaryotes. In Drosophila melanogaster, Dicer-2 (DmDcr-2)-mediated RNAi pathway plays important roles in defending against viral infections and protecting genome integrity. During the maturation of siRNAs, two cofactors can regulate DmDcr-2's functions: Loqs-PD that is required for dsRNA processing, and R2D2 that is essential for the subsequent loading of siRNAs into effector Ago2 to form RISC complexes. However, due to the lack of structural information, it is still unclear whether R2D2 and Loqs-PD affect the functions of DmDcr-2 simultaneously. Here we present several cryo-EM structures of DmDcr-2/R2D2/Loqs-PD complex bound to dsRNAs with various lengths by the Helicase domain. These structures revealed that R2D2 and Loqs-PD can bind to different regions of DmDcr-2 without interfering with each other. Furthermore, the cryo-EM results demonstrate that these complexes can form large oligomers and assemble into fibers. The formation and depolymerization of these oligomers are associated with ATP hydrolysis. These findings provide insights into the structural mechanism of DmDcr-2 and its cofactors during siRNA processing. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8hf0.cif.gz | 669.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8hf0.ent.gz | 530.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8hf0.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 8hf0_validation.pdf.gz | 1.3 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8hf0_full_validation.pdf.gz | 1.3 MB | 表示 | |
XML形式データ | 8hf0_validation.xml.gz | 96.8 KB | 表示 | |
CIF形式データ | 8hf0_validation.cif.gz | 145.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/hf/8hf0 ftp://data.pdbj.org/pub/pdb/validation_reports/hf/8hf0 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 198006.688 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ) 遺伝子: Dcr-2, cg6493, Dcr, dcr, DCR-2, dcr-2, Dcr-2-RA, DCR2, Dcr2, dcr2, dDcr2, dic2, DICER, Dicer, dicer, DICER-2, dicer-2, Dicer2, dicer2, dmDcr-2, Dmel\CG6493, CG6493, Dmel_CG6493 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: A1ZAW0, deoxyribonuclease I, 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エンドリボヌクレアーゼ, ribonuclease III, EC: 3.6.1.3 #2: タンパク質 | | 分子量: 38502.574 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ) 遺伝子: loqs, cg6866, Dmel\CG6866, dRax, loq, LOQS, Loqs, Loqs-PD, LqPD, R3D1, r3d1, R3D1-L, R3D1-S, TRBP, CG6866, Dmel_CG6866 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: M9MRT5 #3: タンパク質 | 分子量: 35115.254 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ) 遺伝子: r2d2, cg7138, Dmel\CG7138, R2D2, R2d2, CG7138, Dmel_CG7138 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q9VLW8 #4: RNA鎖 | 分子量: 16646.871 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: dsRNA 由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ) 発現宿主: Drosophila melanogaster (キイロショウジョウバエ) |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: DmDcr-2/R2D2/LoqsPD with 50bp-dsRNA in Dimer state / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT |
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分子量 | 値: 0.3 MDa / 実験値: NO |
由来(天然) | 生物種: Drosophila melanogaster (キイロショウジョウバエ) |
由来(組換発現) | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
緩衝液 | pH: 8 |
試料 | 濃度: 0.3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 1500 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.19.2_4158: / 分類: 精密化 | ||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.72 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 141544 / アルゴリズム: BACK PROJECTION / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT | ||||||||||||||||||||||||
拘束条件 |
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